Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add reader for Stereo-seq files. #70

Merged
merged 54 commits into from
May 24, 2024
Merged

Add reader for Stereo-seq files. #70

merged 54 commits into from
May 24, 2024

Commits on Jul 18, 2023

  1. Add reader for Stereo-seq data

    @LLehner
    LLehner committed Jul 18, 2023
    Configuration menu
    Copy the full SHA
    504bd9e View commit details
    Browse the repository at this point in the history

Commits on Jul 19, 2023

  1. Fix init

    @LLehner
    LLehner committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    4595f5d View commit details
    Browse the repository at this point in the history

  2. Fix duplicate Key values

    @LLehner
    LLehner committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    21733f8 View commit details
    Browse the repository at this point in the history

  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    8c4e9b8 View commit details
    Browse the repository at this point in the history

  4. Add Key value

    @LLehner
    LLehner committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    093f8c9 View commit details
    Browse the repository at this point in the history

  5. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Jul 19, 2023
    Configuration menu
    Copy the full SHA
    442de55 View commit details
    Browse the repository at this point in the history

Commits on Aug 3, 2023

  1. Add shapes

    @LLehner
    LLehner committed Aug 3, 2023
    Configuration menu
    Copy the full SHA
    a007eb2 View commit details
    Browse the repository at this point in the history

  2. Remove print

    @LLehner
    LLehner committed Aug 3, 2023
    Configuration menu
    Copy the full SHA
    8a61442 View commit details
    Browse the repository at this point in the history

Commits on Aug 7, 2023

  1. Fix radius

    @LLehner
    LLehner committed Aug 7, 2023
    Configuration menu
    Copy the full SHA
    790ac13 View commit details
    Browse the repository at this point in the history

Commits on Aug 19, 2023

  1. Fix constants

    @LLehner
    LLehner committed Aug 19, 2023
    Configuration menu
    Copy the full SHA
    5c24bb2 View commit details
    Browse the repository at this point in the history

Commits on Aug 20, 2023

  1. Update constants and reader

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    8f48b60 View commit details
    Browse the repository at this point in the history

  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    0f3f9d6 View commit details
    Browse the repository at this point in the history

  3. Fix constants

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    8219aa7 View commit details
    Browse the repository at this point in the history

  4. Add dataset identifier

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    ca22756 View commit details
    Browse the repository at this point in the history

  5. Update reader

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    b7b1866 View commit details
    Browse the repository at this point in the history

  6. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    a6df587 View commit details
    Browse the repository at this point in the history

  7. Fix parameters

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    3a78585 View commit details
    Browse the repository at this point in the history

  8. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    e256b0b View commit details
    Browse the repository at this point in the history

  9. Fix parameters

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    edca0d9 View commit details
    Browse the repository at this point in the history

  10. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    fa1fe68 View commit details
    Browse the repository at this point in the history

  11. Fix input parameters

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    14b3b2c View commit details
    Browse the repository at this point in the history

  12. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    d46d4dd View commit details
    Browse the repository at this point in the history

  13. Fix input parameters

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    ef50c98 View commit details
    Browse the repository at this point in the history

  14. Fix input parameters

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    70a1ab4 View commit details
    Browse the repository at this point in the history

  15. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    1d54073 View commit details
    Browse the repository at this point in the history

  16. Fix mypy

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    62ced28 View commit details
    Browse the repository at this point in the history

  17. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    57fcada View commit details
    Browse the repository at this point in the history

  18. Fix input parameters

    @LLehner
    LLehner committed Aug 20, 2023
    Configuration menu
    Copy the full SHA
    8907869 View commit details
    Browse the repository at this point in the history

Commits on Aug 21, 2023

  1. Fix mypy

    @LLehner
    LLehner committed Aug 21, 2023
    Configuration menu
    Copy the full SHA
    f1523ed View commit details
    Browse the repository at this point in the history

Commits on Feb 21, 2024

  1. Fix automatic dataset_id detection

    @LLehner
    LLehner committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    6c6d609 View commit details
    Browse the repository at this point in the history

  2. Update cellbin_gef location and allow multiple mask files

    @LLehner
    LLehner committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    08653ee View commit details
    Browse the repository at this point in the history

  3. Add optional read arguments

    @LLehner
    LLehner committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    422cba9 View commit details
    Browse the repository at this point in the history

  4. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    81b366c View commit details
    Browse the repository at this point in the history

  5. Fix pre-commit

    @LLehner
    LLehner committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    072559a View commit details
    Browse the repository at this point in the history

  6. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LLehner
    LLehner committed Feb 21, 2024
    Configuration menu
    Copy the full SHA
    abc458e View commit details
    Browse the repository at this point in the history

Commits on Feb 23, 2024

  1. Update cellbin_gef location

    @LLehner
    LLehner committed Feb 23, 2024
    Configuration menu
    Copy the full SHA
    6f6dcf7 View commit details
    Browse the repository at this point in the history

Commits on Feb 26, 2024

  1. Fix duplicate key names in images and labels

    @LLehner
    LLehner committed Feb 26, 2024
    Configuration menu
    Copy the full SHA
    10c267a View commit details
    Browse the repository at this point in the history

Commits on May 7, 2024

  1. Merge branch 'main' into Stereo-seq_reader

    @LucaMarconato
    LucaMarconato committed May 7, 2024
    Configuration menu
    Copy the full SHA
    df00ec3 View commit details
    Browse the repository at this point in the history

  2. fix spelling

    @LucaMarconato
    LucaMarconato authored May 7, 2024
    Configuration menu
    Copy the full SHA
    d68ae3b View commit details
    Browse the repository at this point in the history

  3. fixed cellID being nan due to incorrect assigned name

    @LucaMarconato
    LucaMarconato committed May 7, 2024
    Configuration menu
    Copy the full SHA
    ac34e78 View commit details
    Browse the repository at this point in the history

Commits on May 15, 2024

  1. fix metadata

    @LucaMarconato
    LucaMarconato committed May 15, 2024
    Configuration menu
    Copy the full SHA
    1872f11 View commit details
    Browse the repository at this point in the history

Commits on May 16, 2024

  1. wip bin data parsing

    @LucaMarconato
    LucaMarconato committed May 16, 2024
    Configuration menu
    Copy the full SHA
    2b8f70f View commit details
    Browse the repository at this point in the history

  2. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed May 16, 2024
    Configuration menu
    Copy the full SHA
    85fde20 View commit details
    Browse the repository at this point in the history

  3. renamed StereoseqKeys to SK

    @LucaMarconato
    LucaMarconato committed May 16, 2024
    Configuration menu
    Copy the full SHA
    23af1bd View commit details
    Browse the repository at this point in the history

  4. Merge branch 'Stereo-seq_reader' of https://github.com/LLehner/spatia… 

    …ldata-io into Stereo-seq_reader
    @LucaMarconato
    LucaMarconato committed May 16, 2024
    Configuration menu
    Copy the full SHA
    8ee712d View commit details
    Browse the repository at this point in the history

Commits on May 21, 2024

  1. comparing points vs shapes for bins

    @LucaMarconato
    LucaMarconato committed May 21, 2024
    Configuration menu
    Copy the full SHA
    295e1b4 View commit details
    Browse the repository at this point in the history

  2. using points for bins

    @LucaMarconato
    LucaMarconato committed May 21, 2024
    Configuration menu
    Copy the full SHA
    abf1471 View commit details
    Browse the repository at this point in the history

Commits on May 22, 2024

  1. experiment with relabeling; I will remove the code

    @LucaMarconato
    LucaMarconato committed May 22, 2024
    Configuration menu
    Copy the full SHA
    65cddb7 View commit details
    Browse the repository at this point in the history

  2. cleanup

    @LucaMarconato
    LucaMarconato committed May 22, 2024
    Configuration menu
    Copy the full SHA
    e9bfc75 View commit details
    Browse the repository at this point in the history

  3. fix spatialdata dependency

    @LucaMarconato
    LucaMarconato committed May 22, 2024
    Configuration menu
    Copy the full SHA
    3c40d08 View commit details
    Browse the repository at this point in the history

Commits on May 24, 2024

  1. stereoseq fixes

    @LucaMarconato
    LucaMarconato committed May 24, 2024
    Configuration menu
    Copy the full SHA
    579d972 View commit details
    Browse the repository at this point in the history

  2. changelog

    @LucaMarconato
    LucaMarconato committed May 24, 2024
    Configuration menu
    Copy the full SHA
    94112e1 View commit details
    Browse the repository at this point in the history

  3. add stereoseq to readme

    @LucaMarconato
    LucaMarconato authored May 24, 2024
    Configuration menu
    Copy the full SHA
    e1ce1ac View commit details
    Browse the repository at this point in the history

  4. cleanup

    @LucaMarconato
    LucaMarconato committed May 24, 2024
    Configuration menu
    Copy the full SHA
    9cd012c View commit details
    Browse the repository at this point in the history